Re: [ccp4bb]: Difficulties with refmac5 dictionary usage: Problem#1

[Daan van Aalten <dava@davapc1.bioch.dundee.ac.uk>]

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Hi Ethan

Refmac5 has a good automatic dictionary generator, provided you put 
reliable coordinates for your ligand in your PDB file. If it's a new
ligand for which you have no coordinates you could generate those with
something like the PRODRG server 
(http://davapc1.bioch.dundee.ac.uk/prodrg/prodrg.html) which will also
give you an O torsion database to help you fit your ligand to the density.

Daan

On Thu, 1 Nov 2001, Ethan Merritt wrote:

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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Hi all:
> 
> I am having many problems in trying to describe new ligands for use in refmac5 refinement.
> Here is one relatively simple one for which I hope someone knows a workaround.
> 
> By default refmac5 looks in $CLIB/data/monomers/  for monomer libraries.
> If I define a new monomer and place in it a private library, I can have refmac5 look here
> first by adding   LIBIN  ./private_mon_lib.cif    to the command line.
> The problem is that if refmac5 finds some monomer in the standard libraries that
> looks vaguely similar to mine, it insists on using that one instead of the one I explicitly
> specified.  Is there some way to tell it _not_ to second guess my choice of descriptions?
> 
> quick description
> -----------------------------
> 
> Here is a partial listing of the output file:
> 	Dictionary files for restraints : /usr/local/CCP4/asterix/lib/data/monomers/mon*cif
> 	Parameters for new entry and VDW: /usr/local/CCP4/asterix/lib/data/monomers/ener_lib.cif
> 	User supplied dictionary entries: ligands/private_mon_lib.cif
> 	[snip]
>   I am reading library. Please wait.
>                 mon_lib.cif
>   WARNING : monomer looks like ASO     program will use this one
>   WARNING : monomer has the minimal description
>                           program will create complete description
> 
> And then it complains that the geometry is horrible and it is defining a new ligand library f
> or me to check and then it exits.
> 
> More details:
> --------------------
> 
> I actually have ten copies of  the ligand in my structure.  It is quite large,
> and I have not built the entire ligand into all ten sites.  With a great deal of struggle
> I have managed to create a monomer library description for the entire ligand that
> refmac5 accepts, and if the entire ligand is present it will use my library description
> for it.  The problem comes at the sites where some atoms are missing.  Instead of
> simply accepting it a partial fragment of the ligand type I specificy, refmac5 goes
> and hunts in the standard libraries for some other ligand type with the same 
> number of atoms, as shown above.
> 
> -- 
> Ethan A Merritt       merritt@u.washington.edu
> Biomolecular Structure Center Box 357742
> University of Washington, Seattle, WA 98195
> phone: (206)543-1421
> FAX:   (206)685-7002
> 


##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: dava@davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

        O     C           O     C         Visit the PRODRG server to take 
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O   
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "         
       O